Beilstein and Gmelin Databases

Search Overview

  1. Select database from the UW-Madison Libraries web site (if using a library public work station) or launch MDLCrossfire Commander from your computer.
  2. Select either Beilstein or Gmelin or both databases CrossFire COMMANDER window.
    Note: It is possible to search Beilstein and Gmelin simultaneously. If both databases are selected, only structure and text searches are permitted. Predefined Search Forms will not be active because they relate specifically to each database.
  3. Clear previous STRUCTURE or FACT searches if necessary.
  4. Create query.
  5. Transfer query to Commander window
  6. Click on START SEARCH.

Structure/Substructure Search

See Structure/Substructure Search - v. 7 for additional help.

Not all Beilstein and Gmelin substance records include structures. A structure search will eliminate such records. MDL CrossFire Commander 7.0 may be set to use three different structure editors: MDL ISISDraw, MDLDraw, and CrossFire Structure Editor. All UW-Madison Libraries Beilstein Crossfire 7 pages illustrate MDL CrossFire Structure Editor.

  1. Double-click in the STRUCTURE window to switch to Structure mode.
  2. Click on EDIT in the Toolbox.
  3. Draw the structure with the currently active atom (default is C) and bond (default is single), or select one of the ring templates.
  4. Click on an existing atom to open the atom dialog box to modify it.
  5. Set the number of free sites (default is none) and other specifications.
  6. To merge individual structures, select the structure with LASSO or SELECT. Drag the square in the middle of the bond to the target bond or drag the square at the atom node to the target atom. Drag the square at the atom to merge it with another atom.
  7. Click on Return to Commander to return to COMMANDER.
  8. (Optional) Select STRUCTURE QUERY OPTIONS.

Reaction Search

See Reaction Search - v. 7 for additional help.

  1. Begin search in the CrossFire COMMANDER window.
  2. Clear previous STRUCTURE or FACT searches if necessary.
  3. Double-click on STRUCTURE EDITOR to switch to the Structure mode.
  4. Draw structure(s) and/or substructure(s)
  5. Click on REACTION ATTR. Reaction Attributes icon
  6. Define substituents as reactants and products.
  7. Click on Return to Commander window to return to COMMANDER.
  8. Click on START SEARCH.

All-Text Search

All-Text Search provides a text search in all property fields containing text and bibliographic fields.

  1. Type one or several keywords into the SEARCH ALL-TEXT box.
    Note: If more than one keyword is entered in the all-text search field, Commander will run a combined query. The default combination of such phrases is the AND operator but you can overwrite this by entering other operators.
  2. Click on START SEARCH.
  3. Select SEARCH CONTEXT (can select multiple contexts).
  4. Click on START SEARCH.

Displaying Search Results

Disaply view options

  1. Click on VIEW in the SEARCH STATUS REPORT window.
  2. Click on VIEW in the RESULTS window top menu to customize the display.
  3. Click on GO TO NEXT HIT or GO TO PREVIOUS HIT to move to the next or previous record.
  4. Use BACK and FORWARD hyperlinks to move between links to substances, reactions and citations within the record.

Other Display Options

  • Click on SHOW to display structure window.
  • Click on GRID to toggle between substance record display and structure rows and columns display.
  • Click on GET to get related substances, reactions or citations.
  • Click on SORT BY to sort or group the hitset by specified criteria.

Changing Display VIEW

  1. Click on VIEW.
  2. Select Field Availability In Separate Window... or F5.
  3. Check desired fields.
  4. Click on Apply selections to User View.
  5. Click on Close.

Saving Search Results

Hitsets can be temporarily saved on the GLS server and opened for viewing later that day at a library workstation or a personal workstation configured with the Beilstein client. Structures can be saved locally. Saved hitsets and structures drawn with the CrossFire Structure Editor can only be viewed within Beilstein. The FILE menu always applies to the task that is currently active. This includes SAVE.

Saving a hitset

  1. Perform a search.
  2. Click on DISPLAY HITS.
  3. Insert removable storage device (i.e. flash drive, memory stick, 3 1/2" disk ... )
  4. Click on FILE.
  5. Click on SAVE HITSET AS....
  6. Type your disk drive and filename.

Saving a structure

  1. Draw the structure in the Structure Editor.
  2. Insert removable storage device (i.e. flash drive, memory stick, 3 1/2" disk ... )
  3. Click on FILE.
  4. Click on SAVE COPY AS.
  5. Type your disk drive and filename. Beilstein automatically assigns the extension .bsd for CrossFire Structure Editor or .skc for ISISDraw.

Exporting Search Results

EXPORT permits export of structure, reaction and citation data in HTML, Excel or WORD formats. The available pre-defined export settings depend on the record "context". - substance, reaction, or citation. It is possible to create individual export settings for local installations.

  1. Insert removable storage device (i.e. flash drive, memory stick, 3 1/2" disk ... )
  2. Click on EXPORT.
  3. Click on type of data and file format to export.
  4. Click on START.
  5. Type your disk drive and filename.
  6. Click on SAVE.

Exporting Search Results to RefWorks

In Beilstein or Gmelin

  1. Display citation hitset.
  2. Click on Export Hits on the menu bar above the record display.
  3. Click on Procite/Endnote/Reference Manager.
  4. Click in the radio button to select desired records for download.
  5. Click on START.
  6. Save the file as a text file.

In RefWorks

  1. Open your RefWorks account.
  2. Place your cursor over References and click on Import.
  3. Select BIBSYS (RIS Import Format) in the Import Filter/Data Source drop-down menu.
  4. Select All Databases in the Database: drop-down menu.
  5. Select Import Data from the following Text File.
  6. Click on Browse and select the saved .txt file.
  7. Click on Import.
  8. Your citation(s) will automatically be imported into the Last Imported Folder.

Emailing Search Results

  1. Save search results.
  2. Launch your email account.
  3. Attach the file to a message to yourself.

Beginning a New Search, Getting Help, and Exiting

Beginning a New Search

  1. Click on QUERY tab to return to the Commander window.
  2. Click on CLEAR STRUCTURE, CLEAR TABLE, or CLEAR TEXT to clear previous search.

Getting Help

Click on Help for on-screen help. See UW-Madison Beilstein web site.

For further assistance, consult the Chemistry Library staff.


Click on FILE, then EXIT.

Databases Covered

  • Beilstein
  • Gmelin